This TiddlyWiki contains the following tiddlers:
- `deef`: a Shiny app
- $:/_sq/Stories/config/openLinkDivert
- $:/_sq/Stories/config/sidebaroverlaybreakpoint
- $:/_sq/Stories/config/Story2-storyview
- $:/_sq/Stories/Story2StoryList
- $:/.giffmex/.Stylesheet4Stroll
- $:/.giffmex/actions/new-journal
- $:/.giffmex/Buttons/more-tiddler-edit-actions
- $:/.giffmex/EditTemplate/custom
- $:/.giffmex/language/toolbar
- $:/.giffmex/sidebar/advancedconfig
- $:/.giffmex/sidebar/tabs/strollcontrols
- $:/.giffmex/TiddlyBlinkFoldData
- $:/.giffmex/ui/EditTemplate
- $:/.giffmex/ViewTemplate/refscontext
- $:/.giffmex/ViewTemplate/refshidden
- $:/.giffmex/ViewTemplate/refslinks
- $:/.giffmex/ViewTemplate/refstabs
- $:/.giffmex/ViewTemplate/refstranscludeclean
- $:/.giffmex/ViewTemplate/refstranscludecollapse
- $:/.giffmex/ViewTemplate/title
- $:/.giffmex/ViewToolbar/new-note-here
- $:/.giffmex/ViewToolbar/new-note-here-datetime
- $:/build
- $:/config/_sq/Stories/story2
- $:/config/AnimationDuration
- $:/config/AutoSave
- $:/config/codemirror/keyMap
- $:/config/DefaultMoreSidebarTab
- $:/config/DefaultSidebarTab
- $:/config/EditorToolbarButtons/Visibility/$:/core/ui/EditorToolbar/heading-4
- $:/config/EditorToolbarButtons/Visibility/$:/core/ui/EditorToolbar/heading-5
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- $:/config/EditorTypeMappings/text/vnd.tiddlywiki
- $:/config/EmptyStoryMessage
- $:/config/fa5/decorate-extlinks
- $:/config/Navigation/openLinkFromInsideRiver
- $:/config/Navigation/UpdateAddressBar
- $:/config/Navigation/UpdateHistory
- $:/config/NewJournal/Title
- $:/config/PageControlButtons/Visibility/$:/_sq/Stories/Templates/StoryTogglePageControl
- $:/config/PageControlButtons/Visibility/$:/core/ui/Buttons/advanced-search
- $:/config/PageControlButtons/Visibility/$:/core/ui/Buttons/control-panel
- $:/config/PageControlButtons/Visibility/$:/core/ui/Buttons/full-screen
- $:/config/PageControlButtons/Visibility/$:/core/ui/Buttons/home
- $:/config/PageControlButtons/Visibility/$:/core/ui/Buttons/import
- $:/config/PageControlButtons/Visibility/$:/core/ui/Buttons/manager
- $:/config/PageControlButtons/Visibility/$:/core/ui/Buttons/new-image
- $:/config/PageControlButtons/Visibility/$:/core/ui/Buttons/new-journal
- $:/config/PageControlButtons/Visibility/$:/core/ui/Buttons/new-tiddler
- $:/config/PageControlButtons/Visibility/$:/core/ui/Buttons/print
- $:/config/PageControlButtons/Visibility/$:/core/ui/Buttons/refresh
- $:/config/PageControlButtons/Visibility/$:/core/ui/Buttons/storyview
- $:/config/PageControlButtons/Visibility/$:/core/ui/Buttons/tag-manager
- $:/config/PageControlButtons/Visibility/$:/core/ui/Buttons/theme
- $:/config/PageControlButtons/Visibility/$:/core/ui/Buttons/timestamp
- $:/config/Plugins/Disabled/$:/themes/cdr/captivate
- $:/config/Plugins/Disabled/$:/themes/tiddlywiki/snowwhite
- $:/config/RelinkOnRename
- $:/config/SaverFilter
- $:/config/shortcuts/cancel-edit-tiddler
- $:/config/sq/Stories/storyRiverRatio
- $:/config/Tiddlers/TitleLinks
- $:/config/TimestampDisable
- $:/config/Toolbar/Text
- $:/config/ui/EditTemplate
- $:/config/ViewToolbarButtons/Visibility/$:/_sq/Stories/divertTiddlerMacro
- $:/config/ViewToolbarButtons/Visibility/$:/.giffmex/ViewToolbar/new-note-here
- $:/config/ViewToolbarButtons/Visibility/$:/.giffmex/ViewToolbar/new-note-here-datetime
- $:/config/ViewToolbarButtons/Visibility/$:/.giffmex/viewtoolbar/viewrefs
- $:/config/ViewToolbarButtons/Visibility/$:/.giffmex/ViewToolbar/viewrefscheckboxes
- $:/config/ViewToolbarButtons/Visibility/$:/core/ui/Buttons/fold
- $:/config/ViewToolbarButtons/Visibility/$:/core/ui/Buttons/more-tiddler-actions
- $:/config/ViewToolbarButtons/Visibility/$:/core/ui/Buttons/new-journal-here
- $:/config/WikiParserRules/Inline/wikilink
- $:/ControlPanel 1
- $:/ControlPanel 2
- $:/ControlPanel 3
- $:/ControlPanel 4
- $:/ControlPanel 5
- $:/ControlPanel 6
- $:/ControlPanel 7
- $:/core
- $:/core/images/advanced-search-button
- $:/core/images/cancel-button
- $:/core/images/close-button
- $:/core/images/delete-button
- $:/core/images/done-button
- $:/core/images/down-arrow
- $:/core/images/edit-button
- $:/core/images/export-button
- $:/core/images/info-button
- $:/core/images/left-arrow
- $:/core/images/menu-button
- $:/core/images/new-button
- $:/core/images/new-image-button
- $:/core/images/new-journal-button
- $:/core/images/options-button
- $:/core/images/right-arrow
- $:/core/images/save-button
- $:/core/images/up-arrow
- $:/core/ui/Buttons/fold
- $:/core/ui/Buttons/more-page-actions
- $:/core/ui/ControlPanel/StoryView
- $:/core/ui/ControlPanel/StoryView 1
- $:/core/ui/ControlPanel/StoryView 2
- $:/core/ui/EditTemplate
- $:/core/ui/EditTemplate/fields
- $:/core/ui/EditTemplate/tags
- $:/core/ui/EditTemplate/title
- $:/core/ui/EditTemplate/type
- $:/core/ui/MoreSideBar/Recent
- $:/core/ui/SideBar/Recent
- $:/core/ui/ViewTemplate 1
- $:/core/ui/ViewTemplate/tags
- $:/core/ui/ViewTemplate/title
- $:/DefaultTiddlers
- $:/discoverfeed
- $:/favicon.ico
- $:/GitHub/Filename
- $:/GitHub/Path
- $:/GitHub/Repo
- $:/GitHub/Username
- $:/images/fa5/solid/code
- $:/images/fa5/solid/info
- $:/images/fa5/solid/link
- $:/images/fa5/solid/list-ol
- $:/images/fa5/solid/pen
- $:/images/fa5/solid/seedling
- $:/Import
- $:/isEncrypted
- $:/language/Buttons/NewHere/Hint
- $:/language/Buttons/NewJournalHere/Hint
- $:/layout
- $:/matvonTWaddle/batchmanipulator/Stylesheet
- $:/palette
- $:/palettes/CaptivateDark
- $:/palettes/CaptivateLight
- $:/palettes/CaptivateTan
- $:/palettes/Dracula
- $:/palettes/Vanilla 1
- $:/plugins/bangyou/tw-echarts4r
- $:/plugins/bangyou/tw-htmlwidgets
- $:/plugins/bangyou/tw-leaflet
- $:/plugins/BurningTree/hammerwidgets
- $:/plugins/cdr/colorlab
- $:/plugins/danielo515/context/css
- $:/plugins/danielo515/ContextPlugin
- $:/plugins/danielo515/ContextPlugin/Caption
- $:/plugins/danielo515/ContextPlugin/Stylesheet/results
- $:/plugins/danielo515/ContextPlugin/widgets/context.js
- $:/plugins/flibbles/relink
- $:/plugins/flibbles/xml
- $:/plugins/Gk0Wk/sidebar-resizer
- $:/plugins/mermaid-tw5
- $:/plugins/mermaid-tw5/mermaid.min.js
- $:/plugins/mermaid-tw5/wrapper.js
- $:/plugins/orange/mermaid-tw5
- $:/plugins/snowgoon88/edit-comptext
- $:/plugins/snowgoon88/edit-comptext/config
- $:/plugins/sq/editor-autolist
- $:/plugins/sq/spotlight
- $:/plugins/sq/sq-filters
- $:/plugins/sq/Stories
- $:/plugins/sukima/reveal-js
- $:/plugins/sukima/talktimer
- $:/plugins/TheDiveO/FontAwesome
- $:/plugins/tiddlywiki/codemirror
- $:/plugins/tiddlywiki/codemirror-closebrackets
- $:/plugins/tiddlywiki/codemirror-keymap-vim
- $:/plugins/tiddlywiki/codemirror-search-replace
- $:/plugins/tiddlywiki/hammerjs
- $:/plugins/tiddlywiki/highlight
- $:/plugins/tiddlywiki/katex
- $:/plugins/tiddlywiki/markdown
- $:/plugins/wikilabs/link-to-tabs
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- $:/SiteTitle
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- $:/state/http-requests
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- $:/state/tab/moresidebar-1850697562
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- $:/status/IsAnonymous
- $:/status/IsLoggedIn
- $:/status/IsReadOnly
- $:/status/RequireReloadDueToPluginChange
- $:/status/UserName
- $:/StoryList
- $:/tags/EditToolbar
- $:/tags/PageControls
- $:/tags/SideBar
- $:/tags/ViewTemplate
- $:/tags/ViewToolbar
- $:/theme
- $:/themes/cdr/captivate
- $:/themes/cdr/captivate/settings/accent-topbar
- $:/themes/cdr/captivate/settings/color-link
- $:/themes/cdr/captivate/settings/color-primary
- $:/themes/cdr/captivate/settings/color-secondary
- $:/themes/cdr/captivate/settings/palette-theme
- $:/themes/jd/Material
- $:/themes/jd/Material/ConfigDB
- $:/themes/jd/Material/images/overflow-button
- $:/themes/jd/Material/Template/Header-Sidebar
- $:/themes/odin/zacht
- $:/themes/tiddlywiki/heavier
- $:/themes/tiddlywiki/snowwhite
- $:/themes/tiddlywiki/starlight
- $:/themes/tiddlywiki/tight
- $:/themes/tiddlywiki/tight-heavier
- $:/themes/tiddlywiki/vanilla
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- $:/themes/tiddlywiki/vanilla/metrics/bodylineheight
- $:/themes/tiddlywiki/vanilla/metrics/fontsize
- $:/themes/tiddlywiki/vanilla/metrics/lineheight
- $:/themes/tiddlywiki/vanilla/metrics/sidebarwidth
- $:/themes/tiddlywiki/vanilla/metrics/storyleft
- $:/themes/tiddlywiki/vanilla/metrics/storytop
- $:/themes/tiddlywiki/vanilla/options/sidebarlayout
- $:/themes/tiddlywiki/vanilla/options/stickytitles
- $:/view
- $:/wilk/buttons/copy-code
- $:/wilk/css/CopyCodeButton
- 2022-10-24 Blogging in Tiddlywiki
- 2022-10-29 Windows Subsystem for Linux 2; Observables; additions to the wiki; what I'm reading
- 2022-11-08 Python; cheatsheets for R and Git; Bayesian statistics teaching
- 2022-11-19 OpenELIS and open source LIMS; Bayesian statistics articles; cool TiddlyWiki plugins
- 2022-12-04 My own data centre to build a sustainable open source information architecture; Firth's logistic regression; miscellaneous links
- 2023-01-19 Informatics book review; LIMS evaluation; information security self-assessment
- 2023-02-27 Holiday reading; learning R; most frequently bookmarked
- 2023-03-29 Blog makeover; code-switching (R & Python); field epidemiology toolkit; our new AI overlords
- 2023-06-24 Xerte Online Toolkits; k-anonymisation; polars; j'accuse le tidyverse; DHIS 2 API; getting yak shaving done
- 2024-02-03 Back to blogging; RSS feed; p values; SENAITE; 2024 reading
- 2024-10-27 SENAITE rabbithole; Python mon amour; Alles was du wissen muss; causal inferencing; better blogging; Bayesian and other shiny new things
- 2025-03-11 SENAITE progress; Bluesky; home server; AOC; Shiny app; Python apps from R; old blog; LibreELEC; Pop!_OS Linux distro and new desktop computer; causal inference course
- 2025-04-10 DHIS 2 indicators for incidence; a good webinar; backing up servers
- 2025-09-11 Karakeep; Paperless GPT; vibe coding; PeerTube; Kodi; Proxmox upgrade
- 2025-12-31 Out with the old, in with the new; updates, plans and aspirations
- About this blog/wiki
- Adapt or perish: learning the tidyverse
- Add interactive charts to your TiddlyWiki
- Adding multicolumn function output to a data.table
- Adding translated subtitles to video recordings of presentations, using large language models
- Admin page
- Advent of Code 2024: days 1-5
- Advent of Code 2024: days 6-9
- Aggregate data on time
- All tags
- ama-dablam.jpg
- And the time is...
- Ansible first steps
- Automating Bitwarden Send
- Backing up servers and desktops with borgmatic
- Bookmarklet to create Markdown links
- brewer.css
- Bulk creation of data elements in DHIS 2
- Calculating directly standardised rates with data for only some age groups
- ChatGPT
- cheatsheet
- Checklist for setting up a new Ubuntu Server VM in Proxmox to run Docker
- Choosing a study design
- Collider bias
- Combine two dichotomous variables into a single variable with four levels
- Combining R and Python in RStudio
- Command line weather forecast
- Conditional data entry fields in DHIS 2 Tracker
- Convenience R functions for querying the SENAITE API
- COVID-19
- Create .gitignore file from R
- Create a GitLab project (from R)
- Creating a QR code for your wifi
- Creating indicators via the DHIS 2 API
- CV
- Dealing with tiny console text in Proxmox
- debsums
- Deleting unused/empty dashboards and similar in DHIS 2 via the API using R
- DHIS 2 version 3.9 - wow
- DHIS2
- Digital Health Networks
- Downloading maps from DHIS 2 with RSelenium
- Embedding Xerte Online Toolkits e-learning in a Web page - example
- Evaluating laboratory information management systems for low and middle income countries
- Extracting postcodes from text
- Field Epidemiology Toolkit
- Filtering on data.table list columns
- First steps with Observables in Quarto
- First steps with setting up demonstration versions of open source software platforms in the cloud
- Fixing "Get Offline Zip" in Xerte
- Formatting in Quarto
- Fun with file formats: todo.txt and the iCalendar format
- Function for labelling e.g. age groups
- Function to aggregate counts by ISO week from dates, without gaps
- Function to find date of end of ISO week for a date
- Function to look for filenames of form yyyymmddpattern and select one with latest date
- Fundamentals of Data Visualization [free book]
- Generating a random outbreak data set for testing and teaching
- Gentle introduction to Python
- Geocomputation with R [free book]
- Getting Things Done, the todo.txt format and the quest for the perfect productivity system
- Getting Windows Subsystem for Linux to work on Windows laptops
- GettingStarted
- Hardening SSH configuration
- How to follow blogs without RSS feeds
- How to install PeerTube on Ubuntu
- How to learn R (an opinionated view)
- howto
- Implementation considerations: infrastructure (DHIS 2 Academy)
- In which I accidentally submit a pull request to Ozone HIS
- Incidence rates in DHIS 2
- Information Security Self-Assessment
- Installation · SENAITE
- Installing authentication for Google Earth on DHIS 2
- Installing DHIS 2 dependencies on Linux
- Installing OpenELIS laboratory information management system on Ubuntu
- Installing SENAITE laboratory information management system on Ubuntu
- Installing Xerte Online Toolkits on Ubuntu 22.04 Linux
- Interested in Bayesian statistics and want to know more?
- Internal Markdown links to tiddlers with file names containing spaces
- Introduction to Bayesian reasoning and statistical methods
- Introduction to Data Science [free book]
- Is polars faster than data.table?
- k-anonymising data sets with the sdcMicro Shiny app
- Laboratory implementation and IDSR
- link
- Links
- Linux commands you should really know
- Live train times from Alsager to Liverpool
- Live train times from Liverpool to Alsager
- Loading ...
- Machine Learning and Deep Learning - A review for Ecologists (arXiv)
- macro/gimg
- Melting questionnaire data with data.table
- Mermaid fix
- Mermaid.js, a Markdown-friendly diagram tool
- Modifying a SENAITE add-on
- MOOCs
- More fun with ChatGPT
- Most frequently bookmarked
- Multilevel logistic regression in Python
- My 2018 notes on installation of DHIS 2
- My CSS tweaks to Tiddlywiki
- My data.table cheatsheet
- My Docker cheatsheet
- My ggplot2 cheatsheet
- My Git cheatsheet
- My Linux cheatsheet
- My Python cheatsheet
- My R cheatsheet
- My RMarkdown cheatsheet
- My tags
- My tech
- My tech March 2024
- My Vim cheatsheet
- My Vim configuration file
- My Vim settings
- New RSS feed for the blog
- New Tiddlywiki theme: Captivate Theme
- Next steps with Proxmox
- Notes on Firth's logistic regression and model selection
- Notes on new homelab setup
- Notes on Reproducible Analytical Pipelines
- Notes on the data.table package
- Notes on using Bayesian statistics in outbreak investigation
- Oh no! This web page achieves a carbon rating of F
- Online diagram editors
- Online tools which may occasionally be useful
- Open source e-IDSR system architecture diagram
- OpenELIS versus SENAITE as LIMS options
- Outcomes among confirmed cases and a matched comparison group in the Long-COVID in Scotland study [open access]
- Plotly stacked bar chart that works better for hiding categories
- Plotting Likert-style questionnaire responses
- post
- Post-installation checklist for SENAITE
- PostgreSQL cheatsheet
- Posts
- powershell
- Proxmox cheatsheet
- Proxmox: your own data centre
- Public Health Informatics by Sahay et al - notes and reflections
- Quick DHIS 2
- Quick start with SENAITE laboratory information management system configuration
- Quick summary of a variable
- Read Stata labels in R
- Reading
- Recommendations
- Regression tables for Firth’s logistic regression
- Restarting nginx Web server after configuration changes
- Reveal.js presentations in Tiddlywiki
- Rounding like you expect it
- rss-feed
- Running Python apps from R
- SENAITE
- SENAITE setup data diagram
- senaite-setup-data-mermaid
- SENAITE: customising laboratory report content
- Setting up Let’s Encrypt with nginx
- Should I learn Python now I know R?
- sidebar-text-wrap.css
- Simple frequency table with data.table
- snippet
- Starting fail2ban
- Statistical practice in field epidemiology: so many problems, so many solutions
- Statistical Thinking for the 21st Century [free book]
- Strange tidyverse code
- stuff
- Stuff
- Stuff I found from years ago when I was going down a Web development/Print CSS rabbithole
- Tags
- Teaching Bayesian statistics
- The Book of Why by Judea Pearl and Dana Mackenzie: book notes
- The DHIS 2 API - part 1
- The importance of sustainable, secure and coordinated digital health technologies
- The number of words in this blog/wiki/digital garden/notedump/vanity project
- Things you can now do with AI online
- Tiddlywiki timer
- Timeline with mermaid.js
- timeline-with-mermaid.js
- Timezones
- True random numbers and pseudorandom dogs
- Update on progress with SENAITE laboratory information management system configuration
- Updating an Ubuntu server
- Use of Straighteners and Other Hair Products and Incident Uterine Cancer (open access)
- Useful scripts from ChatGPT
- Useful websites for checking if your site is secure
- Using renv in RStudio with Git for reproducible package management
- vim
- Webinar on RapidPro-DHIS2 integration
- Welcome to Paul Cleary's blog/wiki
- wifi.svg
- Windows Subsystem for Linux (WSL2), RStudio, Git, Docker and a Windows laptop
- Xerte Online Toolkits: hiding the Next button for a specified time
- Xerte Online Toolkits: making a quiz pass rate mandatory